In this work we give a detailed account of complementary small angle neutron scattering and x-ray diffraction studies of polymer mediated, self-assembled FePt nanoparticle arrays as a function of annealing temperature. The combination of these two techniques provides significantly greater physical insight than is available using either individually. Since both methods integrate over a large number of particles statistically meaningful data can be obtained in contrast to imaging techniques where typically only small areas are analyzed. The data show that the median particle size increases with annealing at temperatures of 580 degrees C and above. The data also demonstrate that the distribution of particle diameters is significant and increases with annealing temperature. These results allow a comprehensive structural model of the annealed assemblies to be developed in terms of particle sintering and agglomeration. This enhanced understanding will allow new strategies to be pursued in realizing the potential of nanoparticle assemblies as a monodispersed data storage medium.